You do count
by Ranger0fDiscord
Summary: Crossover between Doctor Who/Sherlock. The 11th Doctor meets Molly Hooper who still thinks she doesn't count. So what happens when she meets the Doctor, who shows her she does count? {Not romantic}{Set sometime between Angels Take Manhattan and The Snowmen}
1. Chapter 1

"Are you even paying attention to me?" Andy's voice broke through the silence that hung over the table.

"Hm?" She asked, looking up to her date. She had figured it'd be nice to distract herself for a while, try and get her mind off of Sherlock and what had happened the past year. She'd figured she'd invite Andy out to eat, her treat. She'd be in control of herself again, Molly Hooper dating. But halfway through she'd found that all he said was just white static noise, and she'd drifted. Her mind went away to neverland as she called it, focusing on smaller, indistinct thoughts. Sherlock, John, DI Lestrade, Jim.. Was that even his real name? Could it have just been another lie, like the rest of her damn time with him.

"You're doing it again." Andy snapped at her, causing Molly to jump.

"I'm sorry.." She sighed. He really was nice, he didn't deserve a woman who didn't listen to him and use him as a distraction. "I'm just not feeling good tonight."

"Is it him again?" He asked, looking genuinely concerned.

"Who?" Molly asked, feigning ignorance.

"Oh come off it. Y'know, that fake genius who committed suicide. What was his name again?"

"Sherlock." She murmured, looking down.

"Yeah, that's him. Didn't ya know him?"

"Briefly, yeah. Helped him on a few cases, that was it." She looked out of the window, just wanting to get out of there. "Listen, d'you mind if I pay my share and leave? I'm really not feeling good right now."

"Blimey, yeah sure." Andy said quickly, getting up to try and help her.

"No no. It's fine, I've got it." Standing up, she reached into her purse and took out her wallet "Look.." She said, putting 25 pounds on the table and getting her coat, "I really am sorry about this, but I'll see ya tomorrow, yeah?"

"Yeah. Yeah, yeah. I mean no problem. It's fine. Do what you must." He said hastily, looking awkward as he smiled at her.

"G'night then." She nodded, exiting the quaint restaurant and into the frigid December air. Pulling her coat around her tighter she walked down the street to her flat in the biting cold. Stupid stupid stupid, she thought. If she had stayed then she could have had Andy given her a ride back but that may have given him the wrong idea. Oh well, it wasn't too long of a walk and it was nice to take in the fresh if not cold air around her.

Crossing the street and heading down Turnmill, she thanked God or whoever was out there for pausing the downpour that had pestered London for the past week or so. She was internally debating whether or not the rain would come back tomorrow, and if so how much when she heard the piercing shriek from Benjamin street. Looking down the narrow street she called out hesitantly. "Hello? Anyone there?" Hearing no reply she stepped cautiously into the street, illuminated a soft orange by the occasional street lamps. "Look, if this is some stupid student prank then you can just forget it because this isn't funny." She called out as she walked past Meze Meze and into the wider street. Underneath a tree by St. John's Gardens she saw the broken body on the pavement.

"Oh God.." Molly Hooper, who had seen smashed faces, intestines, brains, bones, every nasty thing you could ever think of was truly disgusted by the sight she had seen. A poor University student, female by the looks of it, was still gurgling as a large, leathery, horrible beast ate her intestines. Leaning against the bricks, she swallowed the urge to throw up. Unfortunately for her the beast, hearing her looked up and growling, spit out a chunk of flesh and stood up and growled at her, slowing making it's way to her. _If this is it then so be it._ She thought, squeezing shut her eyes and backing up.

"Duck!"

Gasping in shock, Molly ducked just as a man dressed in a dark tweed jacket and suit threw a pail of liquid onto the monster, which caused it to cower and shriek, getting to it's knees.

"There we go, nice Hoixy. Good Hoixy." He said, walking cautiously to the cowering monster.

"Wh-What is that?" Molly whispered, warily taking a step forward.

"A Hoix. If I were you I'd go now before anyone else comes." He knelt by the creature, taking out an object similar to a screwdriver and pointing it at the creature.

"And what exactly will you do with that thing?" She asked, not really caring at this point. She just wanted to get home, take a shower, curl up in bed next to Toby and watch Glee until she fell asleep.

"Take it to it's home."

"Which is..?"

"Far away from here." He stood up then, turning to Molly. "What's your name?"

"M-Molly Hooper. I work at the morgue at the hospital not too far from here." She pointed down the street.

"Nice to meet you Molly Hooper. Now go home, make yourself a nice cup of tea and go to sleep."

"Yes, I was just about to." Blushing, she turned around and began to walk down the street before she paused, spinning around and looking at the man. He was taller than her, with dark hair that fell over his forehead and soft, almost boyish features. "I-I didn't get your name."

"You can call me John Smith."

"Got a new one in for ya today, Molly."

"Huh?" Snapped out of her reverie and back into the real, Molly looked up at her boss. She had barely been able to get any sleep at all last night, staying up late tossing and turning with the images of that monster and the mysterious man burned into her mind.

"God Molly, it's all in one ear and out the other today, isn't it?" Abby said, passing by Molly. "What happened with Andy?" She snickered.

"Nothing happened, I went home early. Wasn't feeling well." Hanging up her coat—it was raining again—and putting on her lab coat, she straightened her hair. "So what's up?"

"Some poor gal, found out on Benjamin street not too far from here. Completely mutilated, cannibalism by the looks of it. Third one this month, the police want a full autopsy. Say if there's anything weird to hand it straight over to them, it's all classified info they say. And what's this about Andy?" Molly's boss, Barry asked her.

"It was just a quick dinner and-" She started before she was cut off by Abby.

"Hold up, Benjamin Street you said? Molly, isn't that close to where you live?" Abby looked back at Molly, who froze up.

"Not too far, yeah. Why does it matter?" She asked, a faint smile plastered on her lips.

"Well.. Did ya hear anything?"

"I- I dunno!" Molly snapped out of- what? Fear? Frustration? Protectiveness? Damn it all, why did she feel so secluded from the outer world? Was it because she knew what they didn't. Feeling bad over the shocked looks on Barry and Abby's faces she sighed internally. "Listen, I didn't hear anything. And even if I did don't you think I would've called the police?"

"She has a point." Barry gave Abby a scathing glance, which clearly said "shut up". "Just go ahead and perform the autopsy, will ya Molls?" His voice was gentile and kind, just like Barry.

"Yeah, right. I'll uh, I'll just get on it now." Molly said, rushing into the autopsy room. God did she hate their stares. What if someone found out she had seen the girl get killed? How could she explain that? 'Oh yeah I was just walking home when I was this giant monster eat some girls intestines and then just as he was about to eat me I was saved by some bloke in Victorian era clothes!' They'd lock her up for good. And what kind of name was John Smith anyways? Who was named John Smith in Two thousand bloody twelve?

Sure, he had saved her life but he could've at least explained who he was, and what the hell that thing was. He called it a "Hoix".

Molly shook away her thoughts and set about getting herself ready for the autopsy. It would be just a quick one she mused. After all, most of the poor girls flesh _was_ missing. She began the work of setting up the room for the pathologist. She was his assistant, barely noticed by him. It was a bit irritating to say in the least, after all she was incredibly helpful. Quiet, kind and helping. What more could a Doctor want?

"Hello Molly." Doctor Carter walked into the mortuary, looking as serious as ever. "Shall we get to this then?" He asked, nodding to the body.

"Right." She said, and they got to it. First was the external examination. They went through the normal procedures. Gender, looks, distinguishing features, what not. Then came the internal examination. Molly placed the rubber block down and stepped away, waiting for Doctor Carvers orders.

"We're going to have to go about this one differently.." He murmured, examining the shreds of flesh and organ caked with dried blood.

"What do you suggest?" She asked, glancing up at him.

"We poke around. See if we can find anything in this mess." Sighing, he bent over to look at the gruesome wound. "Hang on a moment.." He stood up, gesturing for Molly to move closer. "Pass me the tweezers, will you?"

"Right." Molly did as he said, stepping closer to him to see what he had found. "What is it?"

"It's a piece of.. Well.. I don't know." He held up the tweezers, which had an almost crystallized, long, orange tooth. The tooth of the monster that had attacked the woman. "What the bloody hell is this?"

"B-Barry said if we find anything strange to give it straight to him so he can give it to the police. Classified info." She said lowly.

"Will you then?" Doctor Carver asked, putting the tooth in an evidence bag and handing it to her. "Be quick, we've still got work to do."

"Will do." Taking the small bag, Molly walked out of the mortuary and up into Barry's office. Knocking the door, she looked down at the small bag. The tooth sat there, looking harmless and innocent. Less than 24 hours ago that tooth's twins had been about to rip her to shreds. She had never even gotten to thank that man. Was he even still alive? Maybe tomorrow she'd be helping Doctor Carver perform a post-mortem on his body.

"Come in." Barry said, and Molly opened the door, stepping through the threshold. "Oh, it's you. What's up Molls?" He asked, leaning forward in his seat.

"You said to bring you anything strange or weird.. So.. Here.." She put the tooth down on his desk and stepping back. "It seems to be some sort of a tooth of some kind.."

"I can see that.." Barry picked it up, looking at it. "But from what though? Oh well.." He set it back down. "I'll hand it over, they can deal with it. Thanks though. If you see anything else just bring it back, alright?"

"Right." She stepped out of his office, heading back down to where she belonged. The rest of the day fell into a haze. They finished the postmortem with no other incident, and she finished her work quickly so she could head home and take time to get over this.

Taking off her labcoat she walked up to her small office space. Gathering up her things she walked up to the main office. She peeked in, seeing only Abby. "Hey, Abby. I'm not feeling so good so I'm going home early. Mind telling Barry for me?" Molly asked, smiling at Abby. While Abby was a bit cruel sometimes, she understood Molly's need for just some alone time. A break from all the death, even if that break was often spent alone.

"Sure thing." Abby replied, not even looking up. That was the other thing Molly loved about Abby. She rarely asked questions. Sure when she did they were very personal, and sometimes rude, and she never stopped. But most of the time Abby was quiet, too distracted to care. A bit like Sherlock, really.

"Thanks." Molly said, walking out. She ducked her head as she walked to her flat, avoiding the glances of the people around her. At this moment, Molly Hooper really couldn't care less about anything except getting home, curling up with Toby and watching Glee. What could be better?

Molly got to her flat, kicking off her shoes and hanging up her coat by the door before walking into the kitchen to get herself a glass of water. Toby hopped up on the counter, meowing at her.

"What?" She asked, looking down at him, stroking his velvet hair. "You have plenty of leftover food and water in your dish." He huffed and hopped down from the counter. Rolling her eyes, Molly grabbed her glass of water and went into the small living room. She sat down on the deep purple couch, turning on her TV and flipping through the channels when the doorbell rang.

"Coming!" Molly said, heaving herself up and walking to the door. "Yes?" She asked as she opened the door, only to have her smile fall as she stared at the army men with red caps pointing guns at her.

"Molly Hooper?" One of them asked.

"Yes..." She whispered, her voice faltering.

"We're UNIT. We have a few questions for you."

**Characters don't belong to me. Please review/send constructive criticism (That doesn't mean "you suck" etc.) Story will be updated every 1-2 weeks depending on how busy I am. Thanks!**


	2. Chapter 2

Molly found herself in a barely-lit, muggy cell. The only light came from a dim, flickering bulb above her. She was sitting on a hard, cold metal chair right by a table of the same metal. Huddling into a ball and rubbing her arms to create friction, she wondered how she could've gotten herself into this position. Suddenly there was a soft clanking, and as the door opened a beam of light flooded the small cell, partially blinding Molly Hooper.

"Molly Hooper?" A soft, feminine voice came from out of the light.

"Yes.." Molly replied, her timid voice weak with fear as a dark shape formed into the figure of a woman. The woman had blonde hair and a kind face. She carried with her a tray which she set down on the table besides Molly.

"No ones going to hurt you Molly." She said as she sat down across from the curled up woman, pulling her jack around her. "I promise you that once you truthfully answer these questions you'll be released." She smiled and nodded at the tray, which contained steak and mashed potatoes with a cup of milk. "Go ahead and eat. It's not the best, but it's not too bad."

Molly looked down at the tray before glancing back up at the woman. "I'd rather just answer the question ma'am." She said, her voice growing a bit stronger.

"Please, call me Kate." Kate said. "And if you insist, lets get started then. What did you do last night?" She asked, and Molly shrugged, trying not to let her fear take over her.

"Dunno. Went out with some friend from work, went home, watched Glee. Fell asleep. Why?" Molly kept her voice even, trying to make sure it wouldn't betray her. If this was about last night then she had to make sure they didn't know she saw anything.

"You didn't see anything unusual? Anyone unusual?" Kate demanded, staring directly at Molly, who held the older woman's gaze.

"I work at a morgue. You'll have to define unusual." She replied, which made Kate laugh. It was so sudden, so unexpected in the dark cell that Molly smiled.

"You're right. I mean alien, Molly. Some animal or beast or phenomenon that you wouldn't normally see."

"Like what?"

"Like.. I don't know. A leathery beast eating a woman? A blue police box that disappeared into thin air?" Molly froze at this, which was the wrong thing to do. Kate smiled in victory. "You can tell us Molly. Did you meet a man called the Doctor?"

"He called himself John Smith." She muttered, looking away.

"Yes." Kate gave her a sympathetic smile. "He does that."

"Why do you need to know anyway?"

"Because we're curious Molly. We know what you saw that night, we know-"

"Then why didn't you just tell me at the start!?" Molly interrupted Kate, glaring at her. "You could've avoided all this trouble." Kate sighed.

"It's never easy. We have to be careful about how we do things like this, you must understand. We can't just go around asking people if they've seen him. It's bad enough that people see and know that there are aliens out there but to run around saying 'Hello! Ever met a man named the Doctor?'. No no. It's much easier to ease it out of people." She replied, looking older than her looks would suggest.

"Maybe for you. But did you ever stop and think about the people who are affected by it?" Molly asked. "Do you even wonder about it? I mean it's not like I wasn't stressed out enough, but then last night I see a woman get killed, almost get killed myself and then you lot come banging through my door demanding that I go with you! What if someone saw me and thought I did something illegal or wrong? What then?" She stared, unflinching at Kate.

"I've given you all I know." She continued. "I was walking down Turnmill Street when I heard a noise from Benjamin street. I walked down it to see what was going on and saw some.. Monster attacking a young girl under a tree by St. John's Gardens. A man came up, calling himself John Smith and took it away. I went home. I went to bed. I woke up. Went to work. Helped performed an autopsy on the girl. Saw the tooth. Turned it in. Went home. You lot came. Now can I please go home?"

The two women looked at each for a brief moment, just a flicker, before Kate looked towards the guards. "Please escort Miss Hooper back to her house." As if on cue two guards walked out of the door and to her. She looked up at them before glancing back to Kate, who nodded her approval. Molly got up slowly, walking out of the cell and out of the UNIT headquarters.

Still in the cell Kate Lethbridge-Stewart got up slowly, looking down the corridor as the Hooper girl left. She wasn't the first and she wouldn't be the last girl to meet the Doctor accidentally, and Kate hope for her sake that it wouldn't end badly.

**Kind of a short chapter, but this felt like the perfect place to wrap it up. The next chapter will be longer, I promise. Reviews are welcome, preferably constructive criticism. **


	3. Chapter 3

**Apologies for the slow update. Testing + writers block= hard to write. **

Molly collapsed on her couch with a sigh. Toby hopped up on the cushion next to her and nudged her hand, meowing loudly. "Yes?" She asked as she scratched behind his ears. He meowed again and hopped off the couch, padding over to his food dish.

"Oh, that's what you want." Looking back on it, Toby hadn't been fed all day. Neither had she. Sighing, she got up slowly and walked over to the small kitchen. She got out a can of tuna and opened it. The sound broke through the silence of her apartment as she put the canned fish in the small blue food dish, then picked up his water bowl and filled it up. While he ate she opened up her fridge and looked around before grabbing old leftover pizza. She ate it slowly, thinking about her earlier ordeal. The Doctor... The Doctor.. Doctor What? Who was he?

Sighing, she threw away the rest of the pizza, what little she had had of her appetite had gone and instead she just felt very tired. Picking up Toby, she walked into her room and set him on her bed then got changed into her pajamas. The soft, fluffy and pink material made her feel comfortable, made her feel safe. Warm. Protected.

Drawing back the comforter to her bed, she curled up in her covers and fell asleep.

The next day was gloomy and overcast. Molly pulled her jacket tighter around her as she walked down the streets. She paused to push back her hair when she felt a hand grab at her wrist, pulling her into a small alleyway.

"Hey!" She said, smacking at the owner of the hand, who cried out.

"Ow! Did you have to hit me?" He said, glaring at her. "I was only trying to get your attention."

"You!" Molly gasped suddenly, then began to hit him with her fists again. "You-" smack "Got-" smack "Me-" smack "Into-" smack "So-" smack "Much-" smack "Trouble!" She finished, stepping back and glaring at the tall, skinny man who was dressed in attire that looked like it was from the Victorian era. _  
_

"Trouble?" He asked, looking back at her and getting in her face. "What kind of trouble? Who's been troubling you, eh?"

"UNIT. Whatever they are." Molly replied, crossing her arms. "And it wasn't pleasant either so you had better fess up right now and tell me who you are." She glared up at him, and he laughed.

"I'm the Doctor."

"Doctor What?"

"If you wish."

"That's not what I meant though. I mean, I know who you are. They told me that. I want to know.. Y'know. .Who you are, are. If that makes sense." She added hastily, looking down in embarrassment.

"You're curious about me, aren't you?" The Doctor asked, looking at her as if he had just now seen her for the first time.

"Wouldn't you be, if you were me?" She shot back, looking away quickly.

"No, I wouldn't. Because I'm smarter than that." He stated, straightening his bow tie.

"Well you owe me." Molly said, crossing her arms. "I want a full explanation, now."

He frowned down at her. "And how do I owe you, exactly?"

"I was dragged out of my apartment and questioned all because of you! It was terrible! I've been through enough already, thank you very much." She paused, on the verge of tears as she thought about what _she _personally had gone through.

"Oh yes, yes. I know all about what you've been through. Helping your friend commit suicide, very clever, very clever indeed." He rocked back on his heels. "And then there was that little romance with Jim Moriarty too. Not very clever."

Molly sat there, shell-shocked. "How-How did you-?"

"Know? I looked you up."

"Then you owe me even more!" She said glaring at him again.

"And how, exactly, do I owe you even more?" He looked incredibly bored, as if he wished to just be done with this conversation.

"Because you looked me up without my permission! That's not okay!" She snapped, smacking his arm again.

"Ow!" He said, looking down at it and back up at her. "That hurts you know."

"Well you deserve it." She said, dropping her voice down to a whisper as she noticed people giving her and The Doctor curious glances.

"Fine. I'll make it up to you. Come with me." He held out his hand for her and she hesitantly took it.

"Where are we going?"

"To see an old friend."

**Please review/leave constructive criticism! Thanks!**


	4. UPDATE

**Update: **

**Sorry for not updating this fic! Writers block sucks, plus I had finals which I had to study and get ready for. Anyways expect an update within a week. (Around July 3rd)**


	5. Chapter 4

**Hey guys! Like I posted earlier, sorry for the _really_ slow update, real life got into the way. (I'm looking at you, League of Legends). Anyways, hopefully I'll be updating this story more! Be a doll and leave me some reviews, eh? **

Upon entering the TARDIS, Molly froze. "What... The hell?" She asked, looking around. The main room was circular and dark, with stairs leading only God knew where. "How is this possible?" She whispered, turning around.

"It's The TARDIS, Time And Relative Dimensions In Space." The Doctor said. "And yes it is, bigger on the inside." He leaned against the console. "Pretty cool, eh?" He grinned at her.

"How's it bigger in here than it is.." She pointed behind her towards the door, "Y'know, out there?"

"Time Lord technology. It's a perception filter. Camouflage." He shrugged and turned to the console, leaving her to stare in awe around her. "Now, let's see. Where were we going to go? Ah yes! To see your good friend, Sherlock Holmes." Molly turned sharply.

"No! We can't go see him!" She exclaimed, rushing forward in an attempt to stop him.

"Why not?" Demanded The Doctor, looking down at her.

She flushed, looking down. "Because I'm not ready to see him yet. And I'm sure he wouldn't be too pleased to see me either. He doesn't like seeing people from his old life, from before..." She pushed back a strand of her hair that had fallen out of her ponytail in embarrassment.

"From before what?" The Doctor persisted.

"Yknow his.." Biting her lip, she looked away.

"His?"

"The thing.."

"Which one?"

"His fall, okay!?" She shouted, backing away.

"Ah.." The Doctor said, rocking back and forth on his heels. "Well, we could go somewhere else you like. If you like. Want? Like. Anyways, all of Time and Space, right here! Well, except for a few places. Fixed points in Time, y'know. But still!"

Molly moved past him and sat on the steps, looking down at her hands in her lap. Sensing the change in her emotions, The Doctor moved in front of her. "He'll be fine, y'know. Your friend."

She sighed, brushing back tears. "I know he will be, but I still see John's face at his funeral when I close my eyes and I can't even tell him that his best friend is alive." She looked up at him. "Do you know what that's like?"

"I know that and more. I've lost people Molly, many people." The Doctor looked down, not meeting her gaze. Sniffing, they stood in silence for a while before Molly piped up.

"Can it really go anywhere?"

"Of course it can." He looked away. "Why, where would you like to go?"

"Anywhere, as long as it's alien." Molly said, getting up and brushing off her coat. Grinning, the taller man turned back to the console and began switching a few levers, moving quickly around.

"Forward or backwards?" He called out, spinning around as he did so.

"Er.. Forwards?" Molly said hesitantly.

Suddenly the floor beneath her began to shake violently as a loud noise made it impossible to speak or hear.

"What's going on!?" She screamed, grabbing onto the nearest railing by her.

"We're travelling!"

"To where!?" She demanded, tightening her grip as the movement threatened to shake her off.

"What?"

"TO. WHERE!?" She yelled as the the movement slowly ceased and the noise died down. The Doctor smiled and pointed at the doors.

"Go out and see."

Slowly, she let go of the railing and stepped forward to the doors. Looking back at The Doctor once for support, she opened the doors and Molly Hooper took her first steps on an alien planet.


End file.
